—

if test -e /usr/local/parabricks/binaries/bin/collectmultiplemetrics ; then python3 -m pip install matplotlib ; fi

if test -e /usr/local/parabricks/TiedHash.pm ; then mv /usr/local/parabricks/TiedHash.pm /etc/perl/ ; fi

parabricks/ /usr/local/parabricks/

—

CUFILE_LOGFILE_PATH=/tmp/cufile.log

PATH=/usr/local/parabricks:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

CUDA_PACKAGE=-12-9 apt update &&
  apt update --fix-missing &&
  apt -y upgrade

CUDA_PACKAGE=-12-9 DEBIAN_FRONTEND=noninteractive apt install --no-install-recommends -y bcftools gds-tools$CUDA_PACKAGE libboost-filesystem-dev libboost-iostreams-dev libboost-program-options-dev libboost-system-dev libbz2-1.0 libcufile-dev$CUDA_PACKAGE libgomp1 libisal2 libjemalloc-dev liblzma5 libtcmalloc-minimal4 perl python3 python3-distlib python3-pip samtools zlib1g libprotobuf-dev

CUDA_PACKAGE=-12-9 apt update &&
  apt update --fix-missing